title: Development of a new resequencing pathogen microarray based assay for detection of broad-spectrum respiratory tract viruses in patients with community-acquired pneumonia.
abstract: A Resequencing Pathogen Microarray (RPM) is a single, highly multiplexed assay for detecting and differentiating similarly related pathogens by using closely overlapping probe sets to determine a target organism's nucleotide sequence. In this study, a new RPM (RPM-IVDC1) that consisted of 224-bp detector tiles corresponding to 9 influenza A subtypes, 11 rhinoviruses, 28 enteroviruses and 38 other respiratory viruses was developed and optimized to provide individual and simultaneous detection sensitivities ranging from 15 to 750 genomic copies for 16 common respiratory pathogens. A total of 110 consecutive patients with community-acquired pneumonia (CAP) admitted to 5 district general hospitals in Beijing during a 1-year period were assessed using the new assay. Among the children (under age 5) and adult patients (above age 18), respiratory syncytial virus (RSV) and rhinovirus (RV) were the most common etiological agents, respectively, which is consistent with reference assays. Atypical pathogens that may cause CAP-like illness, including rubella virus, measles virus, influenza type C virus, human herpesvirus (HHV) were also detected. The results show the capability of RPM-IVDC1 for the accurate detection and identification of multiple virus types, which may be of significant use in epidemic surveillance and outbreak investigations of atypical pathogens.
authors.affiliation: Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China ; Futian District Center for Disease Control and Prevention, Shenzhen, Guangdong, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Shen
authors.forename: Weixian
authors.initials: W
authors.lastname: Shi
authors.forename: Ji
authors.initials: J
authors.lastname: Wang
authors.forename: Miao
authors.initials: M
authors.lastname: Wang
authors.forename: Jin
authors.initials: J
authors.lastname: Li
authors.forename: Chen
authors.initials: C
authors.lastname: Zhang
authors.forename: Kai
authors.initials: K
authors.lastname: Nie
authors.forename: Mengjie
authors.initials: M
authors.lastname: Yang
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.forename: Aihua
authors.initials: A
authors.lastname: Li
authors.forename: Wenjie
authors.initials: W
authors.lastname: Tan
authors.forename: Xuejun
authors.initials: X
authors.lastname: Ma
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D002675:Child, Preschool; D017714:Community-Acquired Infections / Q000175:diagnosis* / Q000821:virology*; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D046228:Microarray Analysis / Q000379:methods*; D008875:Middle Aged; D011014:Pneumonia / Q000175:diagnosis* / Q000821:virology*; D012136:Respiratory Syncytial Viruses / Q000235:genetics; D012137:Respiratory System / Q000821:virology; D012141:Respiratory Tract Infections / Q000175:diagnosis* / Q000821:virology*; D012680:Sensitivity and Specificity; D055815:Young Adult